Marc Perry: Bioinformatics researcher and former graduate student in my lab.Mike Ellison: Professor, University of Alberta (Alberta, Canada) and former graduate student in the lab of my colleague David Pulleyblank.Trevor Moraes: Professor in my department at the University of Toronto and former graduate student with Mike Ellison.Kim (Bird) Ellison: Professor at the University of Alberta, former undergraduate student in my lab (where she met Mike Ellison), Ph.D. at MIT.

Saturday, May 20, 2017

I have read Dance to the Tune of Life. It's a very confusing book for several reasons. Denis Noble has a very different perspective on evolution and what evolutionary theory needs to accomplish. He thinks that life is characterized by something he calls "Biological Relativity." I don't disagree. He also thinks that evolutionary theory needs to incorporate everything that has ever happened in the history of life. That's where we part company.

I'm working slowly on a book about genomes and junk DNA so I was anxious to see how Noble deals with that subject. I tend to judge the quality of books and articles by the way they interpret the controversy over junk DNA. Here's the first mention of junk DNA from page 89. He begins by saying that it's difficult to explain development and the diversity of tissues in multicellular organisms. He continues with,

Thursday, May 18, 2017

Jonathan Wells has written a new book (2017) called Zombie Science: More Icons of Evolution. He revisits his famous Icons of Evolution from 2000 and tries to show that nothing has changed in 17 years.

I wrote a book in 2000 about ten images images, ten "icons of evolution," that did not fit the evidence and were empirically dead. They should have been buried, but they are still with us, haunting our science classrooms and stalking our children. They are part of what I call zombie science.

I won't bore you with the details. The icons fall into two categories: (1) those that were meaningless and/or trivial in 2000 and remain so today, and (2) those that Wells misunderstood in 2000 and are still misunderstood by creationists today.

Tuesday, May 16, 2017

Julia Shaw is a forensic psychologist. She is currently a senior lecturer in criminology at the London South Bank University (London, UK). Shaw is concerned that we are creating a culture where public outreach is being unfairly attacked. Read her Scientific American post at: The Perils of Public Outreach.

Shaw's point is rather interesting. She believes that scientists who participate in public outreach are being unfairly criticized. Let's look closely at her argument.

What scientists write in academic publications is generally intended for a scientific community, full of nuance and precise language. Instead, what scientists say and write in public forums is intended for lay audiences, almost invariably losing nuance but gaining impact and social relevance. This makes statements made in public forums particularly ripe for attack.

by Pierrick Bourrat
Research Fellow, Department of Philosophy
Macquarie University
Sydney, Australia

Both Qiaoying Lu and I are grateful to Professor Moran for the copious attention he has bestowed on our paper. We are early career researchers and didn’t expect our paper to receive so much attention from a senior academic in a public forum. Moran claims that our work is out of touch with science (and more generally works in philosophy of biology), that the paper is weakly argued and that some of what we write is false. But in the end, he puts forward a similar position to ours.

Saturday, May 06, 2017

Qiaoying Lu and Pierrick Bourrat are philosophers in Australia.1 Their research interests include evolutionary theory and they have taken an interest in the current debate over extending evolutionary theory. That debate has been promoted by a small group of scientists who, by and large, are not experts in evolution. They claim that current evolutionary theory—which they define incorrectly as the 1960s version of the Modern Synthesis—needs to be overthrown or extended by including things like epigenetics, niche construction, developmental biology, and plasticity [New Trends in Evolutionary Biology: The Program].

Lu and Bourrat have focused on epigenetics in their recent paper [Debating philosophers: The Lu and Bourrat paper]. They hope to reach an accommodation by re-defining the evolutionary gene as: "any physical structure that causes a heritable variation." Then they go on to say that, "we define the phenotype of an evolutionary gene as everything that the gene makes a difference to when compared to another gene."

By doing this, they claim that epigenetic changes (e.g. transient methylation) fall with the new definition. Therefore, epigenetics doesn't really represent a challenge to evolutionary theory. They explain it like this ....

Wednesday, May 03, 2017

This is the forth post on the Lu and Bourrat paper [Debating philosophers: The Lu and Bourrat paper]. The philosophers are attempting to redefine the word "gene" in order to make epigenetics compatible with current evolutionary theory.

I define a gene in the following way: "A gene is a DNA sequence that is transcribed to produce a functional product" [What Is a Gene?]. This is a biochemical/molecular definition and it's not the same as the definition used in traditional evolution.

Lu and Bourrat discuss the history of the evolutionary gene and conclude,

This is my third post on the Lu and Bourrat (2017) paper [Debating philosophers: The Lu and Bourrat paper]. Part of their argument is to establish that modern evolutionary theory is a gene-centric theory. They need to make this connection because they are about to re-define the word "gene" in order to accommodate epigenetics.

In my last post I referred to their defense of the Modern Synthesis and quoted them as saying that the major tenets of the Modern Synthesis (MS) are still the basis of modern evolutionary theory. They go on to say,

Tuesday, May 02, 2017

I'm discussing a paper by Lu and Bourrat (2017) [Debating philosophers: The Lu and Bourrat paper]. They begin by describing current evolutionary theory, known (to them) as the Modern Synthesis. The paper is about challenges to current evolutionary theory from those who advocate an extended evolutionary synthesis or from those who would replace, rather than extend, current evolutionary theory. It is reasonable to begin with a description of the theory that's being challenged.

John Wilkins posted a link on Facebook to a recent paper by his colleagues in Australia. The authors are Qiaoying Lu of the Department of Philosophy at Macquarie University in Sidney Australia and Pierrick Bourat of the Department of Philosophy at The University of Sydney in Sidney Australia.

Lu, Q., and Bourrat, P. (2017) The evolutionary gene and the extended evolutionary synthesis. The British Journal for the Philosophy of Science, (advanced article) April 20, 2017. [doi: 10.1093/bjps/axw035] [PhilSci Archive]

Abstract: Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance. The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient. We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate. Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘gene’, ‘environment’, and ‘phenotype’ in a way that makes them consistent with gene-centric evolutionary theory. We argue that the evolutionary gene, when being materialized, need not be restricted to nucleic acids but can encompass other heritable units such as epialleles. If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance.

The main criticisms fall into two categories: (1) the primary unit of selection is the individual organism, not the gene, and (2) the book placed too much emphasis on adaptation (Darwinism). I think modern evolutionary theory is based on 21st century population genetics and that view puts a great deal of emphasis on the power of random genetic drift. The evolution of a population involves the survival of individuals within the population and that, in turn, depends on the variation that exists in the population. Thus, evolution is characterized by changes in the frequencies of alleles in a population.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.